2PZX | pdb_00002pzx

Structure of the methuselah ectodomain with peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.407 (Depositor), 0.397 (DCC) 
  • R-Value Work: 
    0.376 (Depositor), 0.372 (DCC) 
  • R-Value Observed: 
    0.376 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2PZX

This is version 1.4 of the entry. See complete history

Literature

Extension of Drosophila melanogaster life span with a GPCR peptide inhibitor.

Ja, W.W.West, A.P.Delker, S.L.Bjorkman, P.J.Benzer, S.Roberts, R.W.

(2007) Nat Chem Biol 3: 415-419

  • DOI: https://doi.org/10.1038/nchembio.2007.2
  • Primary Citation Related Structures: 
    2PZX

  • PubMed Abstract: 

    G protein-coupled receptors (GPCRs) mediate signaling from extracellular ligands to intracellular signal transduction proteins. Methuselah (Mth) is a class B (secretin-like) GPCR, a family typified by their large, ligand-binding, N-terminal extracellular domains. Downregulation of mth increases the life span of Drosophila melanogaster; inhibitors of Mth signaling should therefore enhance longevity. We used mRNA display selection to identify high-affinity (K(d) = 15 to 30 nM) peptide ligands that bind to the N-terminal ectodomain of Mth. The selected peptides are potent antagonists of Mth signaling, and structural studies suggest that they perturb the interface between the Mth ecto- and transmembrane domains. Flies constitutively expressing a Mth antagonist peptide have a robust life span extension, which suggests that the peptides inhibit Mth signaling in vivo. Our work thus provides new life span-extending ligands for a metazoan and a general approach for the design of modulators of this important class of GPCRs.


  • Organizational Affiliation
    • Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, California 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 87.34 kDa 
  • Atom Count: 9,174 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 752 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G-protein coupled receptor Mth
A, B, C, D
188Drosophila melanogasterMutation(s): 0 
Gene Names: mth
UniProt
Find proteins for O97148 (Drosophila melanogaster)
Explore O97148 
Go to UniProtKB:  O97148
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO97148
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.407 (Depositor), 0.397 (DCC) 
  • R-Value Work:  0.376 (Depositor), 0.372 (DCC) 
  • R-Value Observed: 0.376 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.233α = 90
b = 94.233β = 90
c = 173.833γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary